Genetic Variant PVR:c.*834A>C (chr19-44662645-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006505.5(PVR):c.*834A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,318 control chromosomes in the GnomAD database, including 65,482 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.93 ( 65427 hom., cov: 31)

Exomes 𝑓: 0.94 ( 55 hom. )

Consequence

PVR
NM_006505.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640

Publications

29 publications found

Variant links:

Genes affected

PVR (HGNC:9705): (PVR cell adhesion molecule) The protein encoded by this gene is a transmembrane glycoprotein belonging to the immunoglobulin superfamily. The external domain mediates cell attachment to the extracellular matrix molecule vitronectin, while its intracellular domain interacts with the dynein light chain Tctex-1/DYNLT1. The gene is specific to the primate lineage, and serves as a cellular receptor for poliovirus in the first step of poliovirus replication. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

PVR links:

CEACAM19 (HGNC:31951): (CEA cell adhesion molecule 19) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

CEACAM19 links:

CEACAM16-AS1 (HGNC:55317): (CEACAM16, CEACAM19 and PVR antisense RNA 1)

CEACAM16-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006505.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PVR	NM_006505.5	MANE Select	c.*834A>C	3_prime_UTR	Exon 8 of 8	NP_006496.4
PVR	NM_001135768.3		c.*834A>C	3_prime_UTR	Exon 8 of 8	NP_001129240.1
PVR	NM_001135769.3		c.*834A>C	3_prime_UTR	Exon 7 of 7	NP_001129241.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PVR	ENST00000425690.8	TSL:1 MANE Select	c.*834A>C	3_prime_UTR	Exon 8 of 8	ENSP00000402060.2
PVR	ENST00000187830.2	TSL:2	n.*1876A>C	non_coding_transcript_exon	Exon 8 of 8	ENSP00000187830.2
PVR	ENST00000706604.1		n.*2566A>C	non_coding_transcript_exon	Exon 6 of 6	ENSP00000516466.1

Frequencies

GnomAD3 genomes

AF:

0.926

AC:

140828

AN:

152074

Hom.:

65371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.980

Gnomad AMI

AF:

0.862

Gnomad AMR

AF:

0.953

Gnomad ASJ

AF:

0.942

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.978

Gnomad FIN

AF:

0.861

Gnomad MID

AF:

0.984

Gnomad NFE

AF:

0.888

Gnomad OTH

AF:

0.933

GnomAD4 exome

AF:

0.937

AC:

118

AN:

126

Hom.:

Cov.:

AF XY:

0.947

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.929

AC:

104

AN:

112

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.581

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.926

AC:

140942

AN:

152192

Hom.:

65427

Cov.:

AF XY:

0.927

AC XY:

68989

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.980

AC:

40705

AN:

41542

American (AMR)

AF:

0.953

AC:

14563

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.942

AC:

3272

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5179

AN:

5180

South Asian (SAS)

AF:

0.977

AC:

4703

AN:

4814

European-Finnish (FIN)

AF:

0.861

AC:

9106

AN:

10582

Middle Eastern (MID)

AF:

0.983

AC:

289

AN:

294

European-Non Finnish (NFE)

AF:

0.888

AC:

60373

AN:

68010

Other (OTH)

AF:

0.934

AC:

1969

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

527

1055

1582

2110

2637

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

906

1812

2718

3624

4530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.905

Hom.:

47587

Bravo

AF:

0.936

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.1

(source)

PhyloP100

0.064

PromoterAI

0.0062

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over